Shortly before midnight on Tuesday, Stephen P. Morgan left his family’s home in Marblehead, Mass., saying goodbye to his father, who thought that his son was moving to Rhode Island to start life anew.

Mr. Morgan had cleared out almost all of his belongings from the guest bedroom, according to an arrest warrant released Friday. But he left behind a few things, including a full box of ammunition and an empty handgun holster.

By morning, he was in Middletown, Conn., jotting down a new journal entry in a composition book he carried. The warrant said he made a reference to seeing all the beautiful and smart people at Wesleyan University before writing, “I think it okay to kill Jews, and go on a killing spree at this school.” And this: “Kill Johanna. She must die.”

About two hours later, Susan Gerdhart was reaching into her purse to pay for a salad at the Red and Black bookstore cafe when she heard four loud pops. She turned around and saw smoke in the air and bullet casings on the ground and a gunman squeeze off three more rounds. The woman who had been serving her, a 21-year-old Wesleyan junior named Johanna Justin-Jinich, was no longer standing there: she was on the floor moaning, dying from her wounds.

As Mr. Morgan, 29, was brought into a Middletown courtroom Friday to answer to a murder that virtually paralyzed an elite college and a Connecticut town, an incongruous portrait of his life and movements emerged through police documents, public records and interviews. He came from a large churchgoing family and a privileged upbringing in one of Boston’s nicer suburbs. He graduated from an elite Roman Catholic high school for boys before completing an unblemished four-year stint in the Navy.

But upon returning to civilian life in 2003, Mr. Morgan struggled, hopscotching from town to town and holding dead-end jobs, including one as a technician at a garage door company in Colorado Springs, and spending two semesters in 2007 as a nondegree student at the University of Colorado in Boulder before moving back with his parents.

During the summer between those semesters, Mr. Morgan took a course at New York University, the same sexual diversity class in which Ms. Justin-Jinich was enrolled. By the end of it, Ms. Justin-Jinich had complained to the university of harassment, saying that Mr. Morgan called her repeatedly and sent her threatening and insulting e-mail messages.

One person who has reviewed the messages said the relationship appeared to have begun on a friendly footing. It was clear from the messages that they had seen one another outside of class, going out to eat on a few occasions, said the person, who declined to be identified because the person was not authorized to discuss them publicly.

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Johanna Justin-Jinich

But the person said that at one point, Ms. Justin-Jinich went away over a three-day weekend, and Mr. Morgan became enraged, sending her e-mail messages asking where she was and why she was not answering his calls.

He began criticizing her, saying she was not so attractive and making an issue of her being half-Jewish, saying that Jewish people are greedy, and criticizing her for wearing what he said were revealing clothes and flaunting her body, the person who reviewed the e-mail messages said. Mr. Morgan suggested that she needed a lot of attention and said she was behaving like a little girl.

Mr. Morgan, who had lived in Colorado Springs and Boulder, also made comments about how people in those parts of the state looked down on people from the area of Colorado where Ms. Justin-Jinich’s family lived, near Fort Collins.

The university referred the matter to the police, but Mr. Morgan left town, and Ms. Justin-Jinich did not press charges.

It remained unclear whether the two had communicated since then or what could have made him decide to set out almost two years later and hunt her down.

Mr. Morgan appeared in court in a dark violet jumpsuit and with his hands cuffed behind his back. He hung his head, nodding when the judge asked if he understood the charges.

Judge Mary-Margaret Burgdorff of Superior Court raised his bail to $15 million from $10 million, citing the gravity of the crime, the fact that the gunman wore a disguise — eyeglasses and a wig — and the threat he had posed to the community until he turned himself in Thursday night at a convenience store near Middletown.

As Mr. Morgan was led out of the courtroom in shackles, members of his family wept and hugged each other, and his father called out “Steve!” Their son’s eyes and mouth widened as he acknowledged them in the crowded room.

After court, his lawyer, Richard R. Brown, said his client posed no threat to Middletown’s Jewish community or the general public as some feared.

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After attending a vigil for Johanna Justin-Jinich on Friday, a group walked along College Row at Wesleyan University.Credit
George Ruhe for The New York Times

“I can understand why people could be concerned,” he said. Nonetheless, “this was not a random act. The allegations concern a specific target, a specific individual and not the greater Middletown community as a whole.”

He added, “There is no evidence that he had a violent history or a personality disorder.”

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Mr. Morgan, whose father, James, is a venture capitalist, graduated in 1998 from the all-boys St. John’s Preparatory School, which is set on a 175-acre campus in Danvers, Mass.

While most of his classmates groomed themselves for their yearbook pictures and wore jackets and ties, he donned a wrinkled polo shirt and had straggly, overgrown hair. He looked aloof, his mouth slightly agape, not smiling.

Under “Thanks to:”, he entered: “Everyone that helped or attempted to help me to graduate. Since while I’m writing this I can’t be sure this is going to happen.”

People who knew him recalled him being a tennis player. One classmate, Grant Paquin, said Friday, “He was weird-quiet, not shy-quiet. I don’t remember him standing out.”

Instead of heading to college like most of his classmates, Mr. Morgan joined the Navy. Lt. Cmdr. John M. Daniels, a Navy spokesman, said he served on the guided missile cruiser Lake Erie, based at Pearl Harbor, until he left the service, after four years, as a petty officer second class. There was no record of misconduct.

According to the arrest affidavit, James Morgan described his son as “being a loner, quiet, not having many friends.”

He said that Stephen Morgan kept a journal and “he has known him to make anti-Jewish comments.”

It is unclear how the gunman tracked down Ms. Justin-Jinich at the bookstore. The arrest affidavit said he drove there in his car, a red 2001 Nissan Sentra with Colorado plates.

After shooting Ms. Justin-Jinich, the affidavit states, Mr. Morgan escaped on a conveyor belt that ran from the basement to the first floor.

The general manager of the bookstore told a detective that “he saw a white male do a somersault and then jump off the conveyor belt,” the affidavit said.

The man then pointed his gun at the manager and said, “Don’t say anything or I’ll shoot.” The gunman, without his disguise, then fled through double swinging doors, according to the affidavit, but lingered outside long enough to be interviewed briefly by police and let go before anyone knew he was a suspect.

Investigators said they found his journal in a computer bag at the crime scene, along with a laptop and a black 9-millimeter semiautomatic pistol concealed in a T-shirt.

After the shooting, the school warned students not to go outside because of the threats in the journal. Some left town.

On Friday, students and town residents gathered on the Wesleyan campus for a vigil.

Under a hazy gray sky they cried and hugged each other, at one point joining hands and bowing their heads in silence.

The university’s president, Michael S. Roth, urged students to “join together in fellowship” during this difficult time. He added that one of the last papers Ms. Justin-Jinich wrote was on “the dignity of man.”

Mr. Roth said later that the school would “start today to resume our normal rhythms of life,” adding that concerts, sporting events and, yes, finals would go on as scheduled, though with much flexibility for those affected by the tragedy.

A version of this article appears in print on , on Page A1 of the New York edition with the headline: From Prep School and Privilege To a Killing at a University Cafe. Order Reprints|Today's Paper|Subscribe